{"id":"https://openalex.org/W1979573134","doi":"https://doi.org/10.1145/1024074.1024075","title":"ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics","display_name":"ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics","publication_year":2004,"publication_date":"2004-09-01","ids":{"openalex":"https://openalex.org/W1979573134","doi":"https://doi.org/10.1145/1024074.1024075","mag":"1979573134"},"language":"en","primary_location":{"id":"doi:10.1145/1024074.1024075","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1024074.1024075","pdf_url":null,"source":{"id":"https://openalex.org/S163326656","display_name":"ACM Transactions on Mathematical Software","issn_l":"0098-3500","issn":["0098-3500","1557-7295"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Mathematical Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022556908","display_name":"Thierry Matthey","orcid":null},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Thierry Matthey","raw_affiliation_strings":["University of Bergen, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069453041","display_name":"Trevor Cickovski","orcid":"https://orcid.org/0000-0003-2724-6951"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Trevor Cickovski","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072225611","display_name":"Scott Hampton","orcid":"https://orcid.org/0000-0003-3376-4042"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott Hampton","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076529591","display_name":"Alice Ko","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alice Ko","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051853078","display_name":"Qun Ma","orcid":"https://orcid.org/0000-0003-0527-8696"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qun Ma","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039960276","display_name":"Matthew Nyerges","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Nyerges","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047526007","display_name":"Troy Raeder","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Troy Raeder","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012543121","display_name":"Thomas Slabach","orcid":null},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Slabach","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039906501","display_name":"Jes\u00fas A. Izaguirre","orcid":"https://orcid.org/0000-0002-4687-4884"},"institutions":[{"id":"https://openalex.org/I107639228","display_name":"University of Notre Dame","ror":"https://ror.org/00mkhxb43","country_code":"US","type":"education","lineage":["https://openalex.org/I107639228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jes\u00fas A. Izaguirre","raw_affiliation_strings":["University of Notre Dame, Notre Dame, IN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Notre Dame, Notre Dame, IN","institution_ids":["https://openalex.org/I107639228"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.0244,"has_fulltext":false,"cited_by_count":85,"citation_normalized_percentile":{"value":0.96520986,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"30","issue":"3","first_page":"237","last_page":"265"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10037","display_name":"Physics of Superconductivity and Magnetism","score":0.9778000116348267,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10339","display_name":"Advanced Numerical Methods in Computational Mathematics","score":0.9746000170707703,"subfield":{"id":"https://openalex.org/subfields/2206","display_name":"Computational Mechanics"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8201426267623901},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.6290024518966675},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5893662571907043},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.5061931014060974},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5037495493888855},{"id":"https://openalex.org/keywords/rapid-prototyping","display_name":"Rapid prototyping","score":0.4534277617931366},{"id":"https://openalex.org/keywords/code-generation","display_name":"Code generation","score":0.4487145245075226},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.44538065791130066},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.44176802039146423},{"id":"https://openalex.org/keywords/object-oriented-programming","display_name":"Object-oriented programming","score":0.43470150232315063},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.39446017146110535},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3505553603172302},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.31050366163253784},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11189362406730652},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.10375002026557922}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8201426267623901},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.6290024518966675},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5893662571907043},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.5061931014060974},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5037495493888855},{"id":"https://openalex.org/C2780395129","wikidata":"https://www.wikidata.org/wiki/Q1128971","display_name":"Rapid prototyping","level":2,"score":0.4534277617931366},{"id":"https://openalex.org/C133162039","wikidata":"https://www.wikidata.org/wiki/Q1061077","display_name":"Code generation","level":3,"score":0.4487145245075226},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.44538065791130066},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.44176802039146423},{"id":"https://openalex.org/C73752529","wikidata":"https://www.wikidata.org/wiki/Q79872","display_name":"Object-oriented programming","level":2,"score":0.43470150232315063},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.39446017146110535},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3505553603172302},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.31050366163253784},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11189362406730652},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.10375002026557922},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/1024074.1024075","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1024074.1024075","pdf_url":null,"source":{"id":"https://openalex.org/S163326656","display_name":"ACM Transactions on Mathematical Software","issn_l":"0098-3500","issn":["0098-3500","1557-7295"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Mathematical Software","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1.8684","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1.8684","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.nd.edu/~izaguirr/papers/toms_protomol.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W32775768","https://openalex.org/W60615445","https://openalex.org/W76658419","https://openalex.org/W94439627","https://openalex.org/W656827624","https://openalex.org/W1492678924","https://openalex.org/W1543889792","https://openalex.org/W1558960195","https://openalex.org/W1567903304","https://openalex.org/W1568663916","https://openalex.org/W1575059645","https://openalex.org/W1596592269","https://openalex.org/W1649645444","https://openalex.org/W1690771817","https://openalex.org/W1963823520","https://openalex.org/W1971231934","https://openalex.org/W1977482735","https://openalex.org/W1980798903","https://openalex.org/W1988883989","https://openalex.org/W1991939674","https://openalex.org/W1994549640","https://openalex.org/W2001676859","https://openalex.org/W2004157562","https://openalex.org/W2017196167","https://openalex.org/W2017835622","https://openalex.org/W2018058849","https://openalex.org/W2027578254","https://openalex.org/W2035687084","https://openalex.org/W2035720425","https://openalex.org/W2041782224","https://openalex.org/W2041902442","https://openalex.org/W2067174909","https://openalex.org/W2067964076","https://openalex.org/W2080803508","https://openalex.org/W2086634221","https://openalex.org/W2091731899","https://openalex.org/W2093988454","https://openalex.org/W2099598754","https://openalex.org/W2103815459","https://openalex.org/W2104301310","https://openalex.org/W2106140689","https://openalex.org/W2113913163","https://openalex.org/W2125155341","https://openalex.org/W2131786814","https://openalex.org/W2154222939","https://openalex.org/W2157081197","https://openalex.org/W2157268641","https://openalex.org/W2157387245","https://openalex.org/W2181449792","https://openalex.org/W2186284576","https://openalex.org/W2323178299","https://openalex.org/W2476745630","https://openalex.org/W2608641272","https://openalex.org/W2987803397","https://openalex.org/W3023686201","https://openalex.org/W4229666556","https://openalex.org/W4231150350","https://openalex.org/W6601312138"],"related_works":["https://openalex.org/W2121300814","https://openalex.org/W1886613375","https://openalex.org/W4236081792","https://openalex.org/W4250583430","https://openalex.org/W4234406076","https://openalex.org/W2010731026","https://openalex.org/W4311328601","https://openalex.org/W2360893094","https://openalex.org/W4390787808","https://openalex.org/W4231091074"],"abstract_inverted_index":{"ProtoMol":[0],"is":[1,21,35,73,109,115],"a":[2,120],"high-performance":[3],"framework":[4,54],"in":[5,67,105],"C++":[6],"for":[7,13,46,81,89,129,138],"rapid":[8],"prototyping":[9],"of":[10,27,43,78,86,132],"novel":[11],"algorithms":[12,102],"molecular":[14,82],"dynamics":[15,83],"and":[16,29,85,100,124,135,144],"related":[17],"applications.":[18],"Its":[19,71],"flexibility":[20],"achieved":[22],"primarily":[23],"through":[24],"the":[25,68,90],"use":[26],"inheritance":[28],"design":[30,72],"patterns":[31],"(object-oriented":[32],"programming).":[33,52],"Performance":[34],"obtained":[36],"by":[37,62],"using":[38],"templates":[39],"that":[40,58,111,125],"enable":[41],"generation":[42],"efficient":[44,101],"code":[45],"sections":[47],"critical":[48],"to":[49,95,119],"performance":[50,114],"(generic":[51],"The":[53],"encapsulates":[55],"important":[56],"optimizations":[57],"can":[59],"be":[60],"used":[61],"developers,":[63],"such":[64],"as":[65],"parallelism":[66],"force":[69,91],"computation.":[70],"based":[74],"on":[75],"domain":[76],"analysis":[77],"numerical":[79],"integrators":[80],"(MD)":[84],"fast":[87],"solvers":[88],"computation,":[92],"particularly":[93],"due":[94],"electrostatic":[96],"interactions.":[97],"Several":[98],"new":[99],"are":[103,147],"implemented":[104],"ProtoMol.":[106],"Finally,":[107],"it":[108,126],"shown":[110],"ProtoMol's":[112],"sequential":[113],"excellent":[116],"when":[117],"compared":[118],"leading":[121],"MD":[122],"program,":[123],"scales":[127],"well":[128],"moderate":[130],"number":[131],"processors.":[133],"Binaries":[134],"source":[136,151],"codes":[137],"Windows,":[139],"Linux,":[140],"Solaris,":[141],"IRIX,":[142],"HP-UX,":[143],"AIX":[145],"platforms":[146],"available":[148],"under":[149],"open":[150],"license":[152],"at":[153],"http://protomol.sourceforge.net.":[154]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
